Importance of the HSP90 molecular chaperoning pathway for antibody diversification by determining AID stability

La protéine AID (déaminase induite par l’activation) joue un rôle central dans la réponse immunitaire adaptative. En désaminant des désoxycytidines en désoxyuridines au niveau des gènes immunoglobulines, elle initie l’hypermutation somatique (SHM), la conversion génique (iGC) et la commutation isotypique (CSR). Elle est essentielle à une réponse humorale efficace en contribuant à la maturation de l’affinité des anticorps et au changement de classe isotypique. Cependant, son activité mutagénique peut être oncogénique et causer une instabilité génomique propice au développement de cancers et de maladies autoimmunes. Il est donc critique de réguler AID, en particulier ses niveaux protéiques, pour générer une réponse immunitaire efficace tout en minimisant les risques de cancer et d’autoimmunité. Un élément de régulation est le fait qu’AID transite du cytoplasme vers le noyau mais reste majoritairement cytoplasmique à l’équilibre. AID est par ailleurs plus stable dans le cytoplasme que dans le noyau, ce qui contribue à réduire sa présence à proximité de l’ADN. Le but de cette thèse était d’identifier de nouveaux partenaires et déterminants d’AID régulant sa stabilité et ses fonctions biologiques. Dans un premier temps, nous avons identifié AID comme une nouvelle protéine cliente d’HSP90. Nous avons montré qu’HSP90 interagit avec AID dans le cytoplasme, ce qui empêche la poly-ubiquitination d’AID et sa dégradation par le protéasome. En conséquence, l’inhibition d’HSP90 résulte en une diminution significative des niveaux endogènes d’AID et corrèle avec une réduction proportionnelle de ses fonctions biologiques dans la diversification des anticorps mais aussi dans l’introduction de mutations aberrantes. Dans un second temps, nous avons montré que l’étape initiale dans la stabilisation d’AID par la voie de chaperonnage d’HSP90 dépend d’HSP40 et d’HSP70. En particulier, la protéine DnaJa1, qui fait partie de la famille des protéines HSP40s, limite la stabilisation d’AID dans le cytoplasme. La farnésylation de DnaJa1 est importante pour l’interaction entre DnaJa1 et AID et moduler les niveaux de DnaJa1 ou son état de farnésylation impacte à la fois les niveaux endogènes d’AID mais aussi la diversification des anticorps. Les souris DNAJA1-/- présentent une réponse immunitaire compromise en cas d’immunisation, qui est dûe à des niveaux réduits d’AID et un défaut de commutation de classe. Dans un troisième temps, nous avons montré que la protéine AID est intrinsèquement plus instable que sesprotéines paralogues APOBEC. Nous avons identifié l’acide aspartique en seconde position d’AID ainsi qu’un motif semblable au PEST comme des modulateurs de la stabilité d’AID. La modification de ces motifs augmente la stabilité d’AID et résulte en une diversification des anticorps plus efficace. En conclusion, l’instabilité intrinsèque d’AID est un élément de régulation de la diversification des anticorps. Cette instabilité est en partie compensée dans le cytoplasme par l’action protective de la voie de chaperonnage DnaJa1-HSP90. Par ailleurs, l’utilisation d’inhibiteurs d’HSP90 ou de farnésyltransférases pourrait être un outil intéressant pour la modulation indirecte des niveaux d’AID et le traitement de lymphomes/leucémies et de maladies auto-immunes causés par AID.

Probabilité et temps de fixation à l’aide de processus ancestraux

Ce mémoire analyse l’espérance du temps de fixation conditionnellement à ce qu’elle se produise et la probabilité de fixation d’un nouvel allèle mutant dans des populations soumises à différents phénomènes biologiques en uti- lisant l’approche des processus ancestraux. Tout d’abord, l’article de Tajima (1990) est analysé et les différentes preuves y étant manquantes ou incomplètes sont détaillées, dans le but de se familiariser avec les calculs du temps de fixa- tion. L’étude de cet article permet aussi de démontrer l’importance du temps de fixation sur certains phénomènes biologiques. Par la suite, l’effet de la sé- lection naturelle est introduit au modèle. L’article de Mano (2009) cite un ré- sultat intéressant quant à l’espérance du temps de fixation conditionnellement à ce que celle-ci survienne qui utilise une approximation par un processus de diffusion. Une nouvelle méthode utilisant le processus ancestral est présentée afin d’arriver à une bonne approximation de ce résultat. Des simulations sont faites afin de vérifier l’exactitude de la nouvelle approche. Finalement, un mo- dèle soumis à la conversion génique est analysé, puisque ce phénomène, en présence de biais, a un effet similaire à celui de la sélection. Nous obtenons finalement un résultat analytique pour la probabilité de fixation d’un nouveau mutant dans la population. Enfin, des simulations sont faites afin de détermi- nerlaprobabilitédefixationainsiqueletempsdefixationconditionnellorsque les taux sont trop grands pour pouvoir les calculer analytiquement.

Étude de l'organisation fonctionnelle du génome humain par un modèle d'interactions entre les séquences répétitives de type LINE-1

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Étude de l'organisation fonctionnelle du génome humain par un modèle d'interactions entre les séquences répétitives de type LINE-1

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Mutation frequency of non-ESBL phenotype SENTRY (Asia-Pacific) isolates of Klebsiella pneumoniae conversion to an ESBL positive phenotype

Extended spectrum β-lactamases or ESBLs, which are derived from non-ESBL precursors by point mutation of β-lactamase genes (bla), are spreading rapidly all over the world and have caused considerable problems in the treatment of infections caused by bacteria which harbour them. The mechanism of this resistance is not fully understood and a better understanding of these mechanisms might significantly impact on choosing proper diagnostic and treatment strategies. Previous work on SHV β-lactamase gene, blaSHV, has shown that only Klebsiella pneumoniae strains which contain plasmid-borne blaSHV are able to mutate to phenotypically ESBL-positive strains and there was also evidence of an increase in blaSHV copy number. Therefore, it was hypothesised that although specific point mutation is essential for acquisition of ESBL activity, it is not yet enough, and blaSHV copy number amplification is also essential for an ESBL-positive phenotype, with homologous recombination being the likely mechanism of blaSHV copy number expansion. In this study, we investigated the mutation rate of non-ESBL expressing K. pneumoniae isolates to an ESBL-positive status by using the MSS-maximum likelihood method. Our data showed that blaSHV mutation rate of a non-ESBL expressing isolate is lower than the mutation rate of the other single base changes on the chromosome, even with a plasmid-borne blaSHV gene. On the other hand, mutation rate from a low MIC ESBL-positive (≤ 8 µg/mL for cefotaxime) to high MIC ESBL-positive (≥16 µg/mL for cefotaxime) is very high. This is because only gene copy number increase is needed which is probably mediated by homologous recombination that typically takes place at a much higher frequencies than point mutations. Using a subinhibitory concentration of novobiocin, as a homologous recombination inhibitor, revealed that this is the case.

Grassland management and conversion into grassland: effects on soil carbon

Grasslands are heavily relied upon for food and forage production. A key component for sustaining production in grassland ecosystems is the maintenance of soil organic matter (SOM), which can be strongly influenced by management. Many management techniques intended to increase forage production may potentially increase SOM, thus sequestering atmospheric carbon (C). Further, conversion from either cultivation or native vegetation into grassland could also sequester atmospheric carbon. We reviewed studies examining the influence of improved grassland management practices and conversion into grasslands on soil C worldwide to assess the potential for C sequestration. Results from 115 studies containing over 300 data points were analyzed. Management improvements included fertilization (39%), improved grazing management (24%), conversion from cultivation (15%) and native vegetation (15%), sowing of legumes (4%) and grasses (2%), earthworm introduction (1%), and irrigation (1%). Soil C content and concentration increased with improved management in 74% of the studies, and mean soil C increased with all types of improvement. Carbon sequestration rates were highest during the first 40 yr after treatments began and tended to be greatest in the top 10 cm of soil. Impacts were greater in woodland and grassland biomes than in forest, desert, rain forest, or shrubland biomes. Conversion from cultivation, the introduction of earthworms, and irrigation resulted in the largest increases. Rates of C sequestration by type of improvement ranged from 0.11 3.04 Mg C.ha(-1) yr(-1), with a mean of 0.54 Mg C.ha(-1).yr(-1) and were highly influenced by biome type and climate. We conclude that grasslands can act as a significant carbon sink with the implementation of improved management.

The conversion of lignocellulosics to levulinic acid

Biomass represents an abundant and relatively low cost carbon resource that can be utilized to produce platform chemicals such as levulinic acid. Current processing technology limits the cost-effective production of levulinic acid in commercial quantities from biomass. The key to improving the yield and effi ciency of levulinic acid production from biomass lies in the ability to optimize and isolate the intermediate products at each step of the reaction pathway and reduce re-polymerization and side reactions. New technologies (including the use of microwave irradiation and ionic liquids) and the development of highly selective catalysts would provide the necessary step change for the optimization of key reactions. A processing environment that allows the use of biphasic systems and/or continuous extraction of products would increase reaction rates, yields and product quality. This review outlines the chemistry of levulinic acid synthesis and discusses current and potential technologies for producing levulinic acid from lignocellulosics.

Unlocking risk allocation and equitable conversion : reform of the passing of risk in the sale of land

The principles relating to the passing of risk under a contract for the sale of real property would seem to have been long settled. The rule under the general law is that the risk of loss of the subject matter under a contract for the sale of real property passes to the buyer upon the creation of a valid and binding contract. This article considers the origin of that rule, how it developed with the growth of equity, and advances the view that it is anomalous in a modern context of property dealings. In doing so, the article adverts to the variety of statutory mechanisms used to subvert the rule, few of which are of practical value. It concludes that the rule is outmoded in many respects and suggests a number of reforms which might be implemented nationally to bring consistency and simplicity to the issue of damage or destruction of improvements which are the subject of a land contract.

Security constrained economic dispatch considering wind energy conversion systems

The available wind power is stochastic and requires appropriate tools in the OPF model for economic and reliable power system operation. This paper exhibit the OPF formulation with factors involved in the intermittency of wind power. Weibull distribution is adopted to find the stochastic wind speed and power distribution. The reserve requirement is evaluated based on the wind distribution and risk of under/over estimation of the wind power. In addition, the Wind Energy Conversion System (WECS) is represented by Doubly Fed Induction Generator (DFIG) based wind farms. The reactive power capability for DFIG based wind farm is also analyzed. The study is performed on IEEE-30 bus system with wind farm located at different buses and with different wind profiles. Also the reactive power capacity to be installed in the wind farm to maintain a satisfactory voltage profile under the various wind flow scenario is demonstrated.

TS-fuzzy controlled DFIG based wind energy conversion system

This paper focuses on the implementation of the TS (Tagaki-Sugino) fuzzy controller for the active power and the DC capacitor voltage control of the Doubly Fed Induction Generator (DFIG) based wind generator. DFIG system is represented by a third-order model where electromagnetic transients of the stator are neglected. The effectiveness of the TS-fuzzy controller on the rotor speed oscillations and the DC capacitor voltage variations of the DFIG damping controller on converter ratings of the DFIG system is also investigated. The results of the time domain simulation studies are presented to elucidate the effectiveness of the TS-fuzzy controller compared with conventional PI controller in the DFIG system. The proposed TS-fuzzy controller can improve the fault ride through capability of DFIG compared to the conventional PI controller

Catalytic conversion of gases via cation-exchangable alumino-silicate materials

A process for catalytic conversion and/or adsorption of gases inclusive of NOx, SOx, CO2, CO, dioxins and PAHs and combinations thereof wherein said gases may contain particulates which include contacting one or more of such gases with an alumino-silicate material having: a primarily tetrahedrally co-ordinated aluminium as established by the fact that the 27 A1 Magic Angle Spinning (MAS) provides a single peak at 55-58 ppm (FWHM ~23 ppm) relative to Al(H 2 0) 6 3 and (ii) a cation exchange capacity of at least 1 meq 100 in aqueous solution at room temperature.

Recent advances in catalytic/biocatalytic conversion of greenhouse methane and carbon dioxide to methanol and other oxygenates

Methane gas has been identified as the most destructive greenhouse gas (Liu et al., 2004). It was reported that the global warming potential of methane per molecule relative to CO2 is approximately 23 on a 100-year timescale or 62 over a 20-year period (IPCC, 2001). Methane has high C-H bond energy of about 439 kJ/mol and other higher alkanes (or saturated hydrocarbons) also have a very strong C-C and C-H bonds, thus making their molecules to have no empty orbitals of low energy or filled orbitals of high energy that could readily participate in chemical reactions as is the case with unsaturated hydrocarbons such as olefins and alkynes (Crabtree, 1994; Labinger & Bercaw, 2002)...